Chapter 11 Skin microbiota: functional analysis

11.1 MCI

GIFTs_functions_community %>%
  rowMeans() %>%
  as_tibble(., rownames = "sample") %>%
  left_join(sample_metadata, by = join_by(sample == sample)) %>%
#  filter(time_point=="0_Wild") %>%
  group_by(environment) %>%
  summarise(MCI = mean(value), sd = sd(value))
# A tibble: 2 × 3
  environment   MCI     sd
  <fct>       <dbl>  <dbl>
1 low         0.358 0.0521
2 high        0.295 0.0599
MCI <- GIFTs_functions_community %>%
  rowMeans() %>%
  as_tibble(., rownames = "sample") %>%
  left_join(sample_metadata, by = join_by(sample == sample)) 
# %>% 
#   filter(diet!="Post_grass")

shapiro.test(MCI$value)

    Shapiro-Wilk normality test

data:  MCI$value
W = 0.92978, p-value = 0.04846
wilcox.test(value ~ environment, data=MCI)

    Wilcoxon rank sum exact test

data:  value by environment
W = 181, p-value = 0.001367
alternative hypothesis: true location shift is not equal to 0
Permutation test for adonis under reduced model
Terms added sequentially (first to last)
Permutation: free
Number of permutations: 999

adonis2(formula = GIFTs_functions_community_dist ~ environment, data = sample_metadata %>% filter(sample %in% labels(GIFTs_functions_community_dist)) %>% arrange(match(sample, labels(GIFTs_functions_community_dist))), permutations = 999, by = "terms")
            Df SumOfSqs      R2      F Pr(>F)   
environment  1   0.7443 0.19325 6.7072  0.003 **
Residual    28   3.1071 0.80675                 
Total       29   3.8514 1.00000                 
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

11.2 Wilcoxon

11.2.1 Community elements differences:

   Elements         low        high                                      Function
1     B0205 0.656049000 0.475561400             Amino acid biosynthesis_Threonine
2     B0207 0.558104900 0.437034800            Amino acid biosynthesis_Methionine
3     B0208 0.720234000 0.453394600                Amino acid biosynthesis_Valine
4     B0209 0.817868200 0.533705800            Amino acid biosynthesis_Isoleucine
5     B0210 0.743591700 0.450369200               Amino acid biosynthesis_Leucine
6     B0211 0.692446900 0.527403300                Amino acid biosynthesis_Lysine
7     B0212 0.662103100 0.482202700              Amino acid biosynthesis_Arginine
8     B0213 0.658973300 0.404776500               Amino acid biosynthesis_Proline
9     B0214 0.538837000 0.427169000             Amino acid biosynthesis_Glutamate
10    B0215 0.555625900 0.384205800             Amino acid biosynthesis_Histidine
11    B0216 0.656080300 0.398413900            Amino acid biosynthesis_Tryptophan
12    B0218 0.547111400 0.454774400              Amino acid biosynthesis_Tyrosine
13    B0219 0.130706150 0.053109630                  Amino acid biosynthesis_GABA
14    B0220 0.278230900 0.157103900          Amino acid biosynthesis_Beta-alanine
15    B0221 0.611932300 0.441615300             Amino acid biosynthesis_Ornithine
16    B0303 0.262207900 0.219991800    Amino acid derivative biosynthesis_Ectoine
17    B0307 0.331732800 0.190395900 Amino acid derivative biosynthesis_Spermidine
18    B0309 0.163550590 0.066682630 Amino acid derivative biosynthesis_Putrescine
19    B0310 0.324450620 0.096901480 Amino acid derivative biosynthesis_Tryptamine
20    B0601 0.624014300 0.519070800          Organic anion biosynthesis_Succinate
21    B0602 0.822709900 0.702780300           Organic anion biosynthesis_Fumarate
22    B0604 0.442414500 0.663182100          Organic anion biosynthesis_L-lactate
23    B0605 0.345982500 0.192877900          Organic anion biosynthesis_D-lactate
24    B0701 0.634894500 0.480184300            Vitamin biosynthesis_Thiamine (B1)
25    B0702 0.816474800 0.727775100          Vitamin biosynthesis_Riboflavin (B2)
26    B0704 0.695651400 0.423724000        Vitamin biosynthesis_Pantothenate (B5)
27    B0705 0.427025500 0.322247500         Vitamin biosynthesis_Pyridoxal-P (B6)
28    B0707 0.761055800 0.687081300    Vitamin biosynthesis_Tetrahydrofolate (B9)
29    B0708 0.529524200 0.397595900          Vitamin biosynthesis_Cobalamin (B12)
30    B0802 0.834491600 0.525997700        Aromatic compound biosynthesis_Gallate
31    B0803 0.747515200 0.466065500     Aromatic compound biosynthesis_Chorismate
32    B0804 0.713239900 0.564040300   Aromatic compound biosynthesis_Dipicolinate
33    B1029 0.020309560 0.109015400          Antibiotic biosynthesis_Pyrrolnitrin
34    D0101 0.456920700 0.195072900                Lipid degradation_Triglyceride
35    D0204 0.380570100 0.297753100             Polysaccharide degradation_Chitin
36    D0206 0.330051000 0.188121700     Polysaccharide degradation_Alpha galactan
37    D0212 0.347270600 0.568537200           Polysaccharide degradation_Arabinan
38    D0213 0.183368100 0.104352100              Polysaccharide degradation_Mucin
39    D0308 0.195833000 0.100759700                  Sugar degradation_L-Rhamnose
40    D0309 0.318345100 0.222315900                   Sugar degradation_Galactose
41    D0310 0.022423170 0.195423010                       Sugar degradation_NeuAc
42    D0501 0.621591000 0.281872700                 Amino acid degradation_Serine
43    D0505 0.406362500 0.268585000                 Amino acid degradation_Valine
44    D0506 0.413331800 0.225587800             Amino acid degradation_Isoleucine
45    D0507 0.464046400 0.327584800                Amino acid degradation_Leucine
46    D0508 0.327950100 0.201021000                 Amino acid degradation_Lysine
47    D0512 0.453178200 0.259483100              Amino acid degradation_Histidine
48    D0601 0.346266800 0.600710800         Nitrogen compound degradation_Nitrate
49    D0603 0.190956000 0.100831600           Nitrogen compound degradation_Urate
50    D0613 0.770957000 0.465556200         Nitrogen compound degradation_Taurine
51    D0704 0.599817900 0.391382100                  Alcohol degradation_Glycerol
52    D0706 0.002325978 0.005227122           Alcohol degradation_Ethylene glycol
53    D0816 0.254836100 0.147730100          Xenobiotic degradation_Phenylacetate
54    D0907 0.430336700 0.250939200           Antibiotic degradation_Tetracycline
55    D0908 0.313546400 0.169073500              Antibiotic degradation_Macrolide

11.2.2 Community functions differences

   Code_function        low       high                           Function
1            B02 0.60472030 0.45731280            Amino acid biosynthesis
2            B03 0.30395930 0.15951330 Amino acid derivative biosynthesis
3            B06 0.70733810 0.63489430         Organic anion biosynthesis
4            B07 0.49899850 0.41498730               Vitamin biosynthesis
5            B08 0.47988990 0.39738120     Aromatic compound biosynthesis
6            B10 0.07930675 0.11431308            Antibiotic biosynthesis
7            D01 0.49240620 0.39070900                  Lipid degradation
8            D03 0.25054260 0.17263400                  Sugar degradation
9            D05 0.37578760 0.31196260             Amino acid degradation
10           D07 0.37342050 0.27095720                Alcohol degradation
11           D09 0.17066803 0.09778859             Antibiotic degradation

11.2.3 Community domains differences

   Code_domain       low      high
1 Biosynthesis 0.4222222 0.3583441
2  Degradation 0.2852374 0.2242999